/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
import MCview.*;
import jalview.ws.DBRefFetcher;
import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.Rectangle;
import java.awt.BorderLayout;
import java.awt.Dimension;
-public class SequenceFetcher
-extends JPanel implements Runnable
+public class SequenceFetcher extends JPanel implements Runnable
{
- ASequenceFetcher sfetch;
+ // ASequenceFetcher sfetch;
JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
AlignFrame alignFrame;
+
StringBuffer result;
+
final String noDbSelected = "-- Select Database --";
+
Hashtable sources = new Hashtable();
- public SequenceFetcher(AlignFrame af)
+
+ private static jalview.ws.SequenceFetcher sfetch = null;
+
+ private static String dasRegistry = null;
+
+ private static boolean _initingFetcher = false;
+
+ private static Thread initingThread = null;
+
+ /**
+ * Blocking method that initialises and returns the shared instance of the
+ * SequenceFetcher client
+ *
+ * @param guiWindow
+ * - where the initialisation delay message should be shown
+ * @return the singleton instance of the sequence fetcher client
+ */
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+ final IProgressIndicator guiWindow)
+ {
+ if (_initingFetcher && initingThread != null && initingThread.isAlive())
+ {
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ // initting happening on another thread - so wait around to see if it
+ // finishes.
+ while (_initingFetcher && initingThread != null
+ && initingThread.isAlive())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ }
+ if (sfetch == null
+ || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ {
+ _initingFetcher = true;
+ initingThread = Thread.currentThread();
+ /**
+ * give a visual indication that sequence fetcher construction is occuring
+ */
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ sfetch = sf;
+ _initingFetcher = false;
+ initingThread = null;
+ }
+ return sfetch;
+ }
+
+ public SequenceFetcher(IProgressIndicator guiIndic)
{
- alignFrame = af;
- sfetch = new jalview.ws.SequenceFetcher();
+ final IProgressIndicator guiWindow = guiIndic;
+ final SequenceFetcher us = this;
+ // launch initialiser thread
+ Thread sf = new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ if (getSequenceFetcherSingleton(guiWindow) != null)
+ {
+ us.initGui(guiWindow);
+ }
+ else
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Could not create the sequence fetcher client. Check error logs for details.",
+ "Couldn't create SequenceFetcher",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ });
+
+ // raise warning dialog
+ }
+ }
+ });
+ sf.start();
+ }
+
+ /**
+ * called by thread spawned by constructor
+ *
+ * @param guiWindow
+ */
+ private void initGui(IProgressIndicator guiWindow)
+ {
+ this.guiWindow = guiWindow;
+ if (guiWindow instanceof AlignFrame)
+ {
+ alignFrame = (AlignFrame) guiWindow;
+ }
+
database.addItem(noDbSelected);
/*
- * Dynamically generated database list
- * will need a translation function from
- * internal source to externally distinct names.
- * UNIPROT and UP_NAME are identical DB sources,
- * and should be collapsed.
+ * Dynamically generated database list will need a translation function from
+ * internal source to externally distinct names. UNIPROT and UP_NAME are
+ * identical DB sources, and should be collapsed.
*/
-
- String dbs[] = sfetch.getSupportedDb();
- for (int i=0; i<dbs.length;i++)
+
+ String dbs[] = sfetch.getOrderedSupportedSources();
+ for (int i = 0; i < dbs.length; i++)
{
if (!sources.containsValue(dbs[i]))
- {
+ {
String name = sfetch.getSourceProxy(dbs[i]).getDbName();
// duplicate source names are thrown away, here.
if (!sources.containsKey(name))
database.addItem(name);
}
// overwrite with latest version of the retriever for this source
- sources.put(name, dbs[i]);
+ sources.put(name, dbs[i]);
}
}
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
frame.setContentPane(this);
if (new jalview.util.Platform().isAMac())
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
}
}
private String getFrameTitle()
{
- return ( (alignFrame == null) ? "New " : "Additional ") +
- "Sequence Fetcher";
+ return ((alignFrame == null) ? "New " : "Additional ")
+ + "Sequence Fetcher";
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
this.setLayout(borderLayout2);
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ database.setFont(JvSwingUtils.getLabelFont());
+ dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(
- "Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation
+ .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ replacePunctuation.setText("Replace commas with semi-colons");
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
ok_actionPerformed();
}
});
+ clear.setText("Clear");
+ clear.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clear_actionPerformed();
+ }
+ });
+
+ example.setText("Example");
+ example.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ example_actionPerformed();
+ }
+ });
close.setText("Close");
close.addActionListener(new ActionListener()
{
close_actionPerformed(e);
}
});
- textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
public void keyPressed(KeyEvent e)
{
- if(e.getKeyCode()==KeyEvent.VK_ENTER)
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
ok_actionPerformed();
}
});
jPanel3.setLayout(borderLayout1);
borderLayout1.setVgap(5);
jPanel1.add(ok);
+ jPanel1.add(example);
+ jPanel1.add(clear);
jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
- jPanel2.add(database);
+ jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
+ jPanel2.setLayout(borderLayout3);
+
+ database.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ db = sfetch.getSourceProxy((String) sources.get(database
+ .getSelectedItem()));
+ String eq = db.getTestQuery();
+ dbeg.setText("Example query: " + eq);
+ replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+ });
+ dbeg.setText("");
+ jPanel2.add(database, java.awt.BorderLayout.NORTH);
+ jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+ jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
+ // jPanel2.setPreferredSize(new Dimension())
jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
- jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ this.add(jPanel2, java.awt.BorderLayout.NORTH);
jScrollPane1.getViewport().add(textArea);
}
+ protected void example_actionPerformed()
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ db = sfetch.getSourceProxy((String) sources.get(database
+ .getSelectedItem()));
+ textArea.setText(db.getTestQuery());
+ } catch (Exception ex)
+ {
+ }
+ jPanel3.repaint();
+ }
+
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ jPanel3.repaint();
+ }
+
+ JLabel dbeg = new JLabel();
+
JComboBox database = new JComboBox();
+
JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = new JButton();
+
JButton close = new JButton();
+
JPanel jPanel1 = new JPanel();
+
JTextArea textArea = new JTextArea();
+
JScrollPane jScrollPane1 = new JScrollPane();
+
JPanel jPanel2 = new JPanel();
+
JPanel jPanel3 = new JPanel();
+
+ JPanel jPanel4 = new JPanel();
+
BorderLayout borderLayout1 = new BorderLayout();
+
BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
public void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
public void ok_actionPerformed()
{
error += "Please select the source database\n";
}
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ // TODO: make this transformation more configurable
+ com.stevesoft.pat.Regex empty;
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ empty = new com.stevesoft.pat.Regex(
+ // replace commas and spaces with a semicolon
+ "(\\s|[,; ])+", ";");
+ }
+ else
+ {
+ // just turn spaces and semicolons into single semicolons
+ empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ }
textArea.setText(empty.replaceAll(textArea.getText()));
- if (textArea.getText().length() == 0)
+ // see if there's anthing to search with
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ .getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
resetDialog();
return;
}
- AlignmentI aresult=null;
- try {
- aresult = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()))
- .getSequenceRecords(textArea.getText());
- }
- catch (Exception e)
- {
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- //error +="Couldn't retrieve sequences from "+database.getSelectedItem();
- System.err.println("Retrieval failed for source ='"+database.getSelectedItem()+"' and query\n'"+textArea.getText()+"'\n");
- e.printStackTrace();
- }
- if (aresult!=null)
- {
- parseResult(aresult, null, null);
- }
- resetDialog();
- }
- /*
- result = new StringBuffer();
- if (database.getSelectedItem().equals("Uniprot"))
- {
- getUniprotFile(textArea.getText());
- }
- else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
+ ArrayList<String> aresultq=new ArrayList<String>();
+ ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+ Object source = database.getSelectedItem();
+ Enumeration en = new StringTokenizer(textArea.getText(), ";");
+ boolean isAliSource=false;
+ try
{
- String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
- ? jalview.datamodel.DBRefSource.EMBLCDS
- : jalview.datamodel.DBRefSource.EMBL;
-
- StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
- SequenceI[] seqs = null;
- while(st.hasMoreTokens())
+ guiWindow.setProgressBar(
+ "Fetching Sequences from " + database.getSelectedItem(),
+ Thread.currentThread().hashCode());
+ DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
+ .get(source));
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ if (proxy.getAccessionSeparator() == null)
{
- EBIFetchClient dbFetch = new EBIFetchClient();
- String qry = database.getSelectedItem().toString().toLowerCase(
- ) + ":" + st.nextToken();
- File reply = dbFetch.fetchDataAsFile(
- qry,
- "emblxml",null);
-
- jalview.datamodel.xdb.embl.EmblFile efile=null;
- if (reply != null && reply.exists())
+ while (en.hasMoreElements())
{
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
- }
- if (efile!=null) {
- for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
- EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
- if (seqparts!=null) {
- SequenceI[] newseqs = null;
- int si=0;
- if (seqs==null) {
- newseqs = new SequenceI[seqparts.length];
- } else {
- newseqs = new SequenceI[seqs.length+seqparts.length];
-
- for (;si<seqs.length; si++) {
- newseqs[si] = seqs[si];
- seqs[si] = null;
- }
- }
- for (int j=0;j<seqparts.length; si++, j++) {
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
+ String item = (String) en.nextElement();
+ try
+ {
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
}
- seqs=newseqs;
}
- }
- } else {
- result.append("# no response for "+qry);
- }
- }
- if (seqs!=null && seqs.length>0) {
- if (parseResult(new Alignment(seqs), null, null)!=null)
- {
- result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
- }
- }
- }
- else if (database.getSelectedItem().equals("PDB"))
- {
- StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
- String query;
- SequenceI[] seqs = null;
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
- {
- SequenceI[] seqparts = getPDBFile(query.toUpperCase());
- if (seqparts != null)
- {
- if (seqs == null)
- {
- seqs = seqparts;
- }
- else
- {
- SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
- int i=0;
- for (; i < seqs.length; i++)
+
+ AlignmentI indres = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
{
- newseqs[i] = seqs[i];
- seqs[i] = null;
+ new OOMWarning("fetching " + item + " from "
+ + database.getSelectedItem(), oome, this);
}
- for (int j=0;j<seqparts.length; i++, j++)
+ if (indres != null)
{
- newseqs[i] = seqparts[j];
+ aresultq.add(item);
+ aresult.add(indres);
}
- seqs=newseqs;
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + source, e);
}
- result.append("# Success for "+query.toUpperCase()+"\n");
- }
- }
- if (seqs != null && seqs.length > 0)
- {
- if (parseResult(new Alignment(seqs), null, null)!=null)
- {
- result.append(
- "# Successfully parsed the PDB File Queries into an Alignment");
- }
- }
- }
- else if( database.getSelectedItem().equals("PFAM"))
- {
- try
- {
- result.append(new FastaFile(
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
- + textArea.getText().toUpperCase(), "URL").print()
- );
-
- if(result.length()>0)
- {
- parseResult( result.toString(), textArea.getText().toUpperCase() );
- }
-
- }
- catch (java.io.IOException ex)
- {
- result = null;
- }
- }
-
- if (result == null || result.length() == 0)
- {
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- }
-
- resetDialog();
- return;
- }
-
- void getUniprotFile(String id)
- {
- EBIFetchClient ebi = new EBIFetchClient();
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-
- DBRefFetcher dbref = new DBRefFetcher();
- Vector entries = dbref.getUniprotEntries(file);
-
- if (entries != null)
- {
- //First, make the new sequences
- Enumeration en = entries.elements();
- while (en.hasMoreElements())
- {
- UniprotEntry entry = (UniprotEntry) en.nextElement();
-
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
- en2 = entry.getName().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
-
- if (entry.getProtein() != null)
- {
- name.append(" " + entry.getProtein().getName().elementAt(0));
}
-
- result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- "\n");
-
}
-
- //Then read in the features and apply them to the dataset
- Alignment al = parseResult(result.toString(), null);
- for (int i = 0; i < entries.size(); i++)
+ else
{
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- Enumeration e = entry.getDbReference().elements();
- Vector onlyPdbEntries = new Vector();
- while (e.hasMoreElements())
+ StringBuffer multiacc = new StringBuffer();
+ while (en.hasMoreElements())
{
- PDBEntry pdb = (PDBEntry) e.nextElement();
- if (!pdb.getType().equals("PDB"))
+ multiacc.append(en.nextElement());
+ if (en.hasMoreElements())
{
- continue;
+ multiacc.append(proxy.getAccessionSeparator());
}
-
- onlyPdbEntries.addElement(pdb);
}
-
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
+ try
{
- al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- DBRefSource.UNIPROT,
- "0",
- en2.nextElement().toString()));
- }
-
-
-
-
- al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
+ aresultq.add(multiacc.toString());
+ aresult.add(proxy.getSequenceRecords(multiacc.toString()));
+ } catch (OutOfMemoryError oome)
{
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
- }
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
+
}
- }
- }
- SequenceI[] getPDBFile(String id)
- {
- Vector result = new Vector();
- String chain = null;
- if (id.indexOf(":") > -1)
+ } catch (Exception e)
{
- chain = id.substring(id.indexOf(":") + 1);
- id = id.substring(0, id.indexOf(":"));
- }
-
- EBIFetchClient ebi = new EBIFetchClient();
- String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
- getAbsolutePath();
- if (file == null)
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
+ // error +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ System.err.println("Retrieval failed for source ='"
+ + database.getSelectedItem() + "' and query\n'"
+ + textArea.getText() + "'\n");
+ e.printStackTrace();
+ } catch (OutOfMemoryError e)
{
- return null;
+ // resets dialog box - so we don't use OOMwarning here.
+ showErrorMessage("Out of Memory when retrieving "
+ + textArea.getText()
+ + " from "
+ + database.getSelectedItem()
+ + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ showErrorMessage("Serious Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ e.printStackTrace();
}
- try
+ if (aresult != null && aresult.size()>0)
{
- PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
- {
- if (chain == null ||
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.
- toUpperCase().equals(chain))
+ AlignmentI ar=null;
+ if (isAliSource) {
+ // new window for each result
+ while (aresult.size()>0)
{
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
- // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
- SequenceI sq = pdbchain.sequence;
- // Specially formatted name for the PDB chain sequences retrieved from the PDB
- sq.setName("PDB|"+id+"|"+sq.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry();
- // Construct the PDBEntry
- entry.setId(id);
- if (entry.getProperty() == null)
- entry.setProperty(new Hashtable());
- entry.getProperty().put("chains",
- pdbchain.id
- + "=" + sq.getStart()
- + "-" + sq.getEnd());
- sq.getDatasetSequence().addPDBId(entry);
- *
- // Add PDB DB Refs
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
- DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,
- "0", id + pdbchain.id);
- sq.addDBRef(dbentry);
- // and add seuqence to the retrieved set
- result.addElement(sq.deriveSequence());
+ parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
}
- }
-
- if (result.size() < 1)
- {
- throw new Exception("WsDBFetch for PDB id resulted in zero result size");
- }
- }
- catch (Exception ex) // Problem parsing PDB file
- {
- jalview.bin.Cache.log.warn("Exception when retrieving " +
- textArea.getText() + " from " +
- database.getSelectedItem(), ex);
- return null;
+ } else {
+ // concatenate all results in one window
+ while (aresult.size()>0)
+ {
+ if (ar==null) { ar = aresult.remove(0);}
+ else { ar.append(aresult.remove(0)); };
+ }
+ parseResult(ar, null, null);
+ }
}
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ resetDialog();
+ }
-
- SequenceI[] results = new SequenceI[result.size()];
- for (int i = 0, j = result.size(); i < j; i++)
- {
- results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null,i);
- }
- return results;
- }*/
+ /*
+ * result = new StringBuffer(); if
+ * (database.getSelectedItem().equals("Uniprot")) {
+ * getUniprotFile(textArea.getText()); } else if
+ * (database.getSelectedItem().equals("EMBL") ||
+ * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
+ * database.getSelectedItem().equals("EMBLCDS") ?
+ * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
+ *
+ * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
+ * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch
+ * = new EBIFetchClient(); String qry =
+ * database.getSelectedItem().toString().toLowerCase( ) + ":" +
+ * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
+ *
+ * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
+ * reply.exists()) { efile =
+ * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null)
+ * { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
+ * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
+ * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
+ * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
+ * SequenceI[seqparts.length]; } else { newseqs = new
+ * SequenceI[seqs.length+seqparts.length];
+ *
+ * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
+ * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
+ * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
+ * seqs=newseqs; } } } else { result.append("# no response for "+qry); } } if
+ * (seqs!=null && seqs.length>0) { if (parseResult(new Alignment(seqs), null,
+ * null)!=null) { result.append("# Successfully parsed the
+ * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
+ * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
+ * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
+ * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
+ * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
+ * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
+ * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
+ * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int
+ * j=0;j<seqparts.length; i++, j++) { newseqs[i] = seqparts[j]; }
+ * seqs=newseqs; } result.append("# Success for "+query.toUpperCase()+"\n"); }
+ * } if (seqs != null && seqs.length > 0) { if (parseResult(new
+ * Alignment(seqs), null, null)!=null) { result.append( "# Successfully parsed
+ * the PDB File Queries into an
+ * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
+ * try { result.append(new FastaFile(
+ * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
+ * textArea.getText().toUpperCase(), "URL").print() );
+ *
+ * if(result.length()>0) { parseResult( result.toString(),
+ * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
+ * result = null; } }
+ *
+ * if (result == null || result.length() == 0) { showErrorMessage("Error
+ * retrieving " + textArea.getText() + " from " + database.getSelectedItem());
+ * }
+ *
+ * resetDialog(); return; }
+ *
+ * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
+ * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+ *
+ * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
+ * dbref.getUniprotEntries(file);
+ *
+ * if (entries != null) { //First, make the new sequences Enumeration en =
+ * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
+ * (UniprotEntry) en.nextElement();
+ *
+ * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
+ * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
+ * name.append("|"); name.append(en2.nextElement()); } en2 =
+ * entry.getName().elements(); while (en2.hasMoreElements()) {
+ * name.append("|"); name.append(en2.nextElement()); }
+ *
+ * if (entry.getProtein() != null) { name.append(" " +
+ * entry.getProtein().getName().elementAt(0)); }
+ *
+ * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
+ * "\n"); }
+ *
+ * //Then read in the features and apply them to the dataset Alignment al =
+ * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
+ * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
+ * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
+ * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
+ * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
+ *
+ * onlyPdbEntries.addElement(pdb); }
+ *
+ * Enumeration en2 = entry.getAccession().elements(); while
+ * (en2.hasMoreElements()) {
+ * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+ * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
+ *
+ *
+ *
+ *
+ * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
+ * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
+ * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
+ * e.nextElement(); sf.setFeatureGroup("Uniprot");
+ * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } }
+ * }
+ *
+ * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
+ * chain = null; if (id.indexOf(":") > -1) { chain =
+ * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
+ *
+ * EBIFetchClient ebi = new EBIFetchClient(); String file =
+ * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file
+ * == null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
+ * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
+ * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
+ * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
+ * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
+ * Sequence - who's dataset includes any special features added from the PDB
+ * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
+ * PDB chain sequences retrieved from the PDB
+ * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
+ * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
+ * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
+ * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
+ * DBRefEtntry because we have obtained the PDB file from a verifiable source
+ * // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ * information DBRefEntry dbentry = new
+ * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
+ * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
+ * result.addElement(sq.deriveSequence()); } }
+ *
+ * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
+ * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file
+ * { jalview.bin.Cache.log.warn("Exception when retrieving " +
+ * textArea.getText() + " from " + database.getSelectedItem(), ex); return
+ * null; }
+ *
+ *
+ * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
+ * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
+ * result.setElementAt(null,i); } return results; }
+ */
AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
sequences = null;
try
{
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
+ sequences = new FormatAdapter().readFile(result.toString(),
+ "Paste", format);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
- if (sequences!=null)
+ if (sequences != null)
{
return parseResult(sequences, title, format);
}
}
else
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
}
return null;
}
- AlignmentI parseResult(AlignmentI al, String title, String currentFileFormat)
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently selected source and settings
+ */
+ public String getDefaultRetrievalTitle() {
+ return "Retrieved from " + database.getSelectedItem();
+ }
+ AlignmentI parseResult(AlignmentI al, String title,
+ String currentFileFormat)
{
if (al != null && al.getHeight() > 0)
{
if (alignFrame == null)
{
- AlignFrame af = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- if (currentFileFormat!=null)
+ AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat != null)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
+ // FORMAT FOR
+ // NON-FormatAdapter Sourced
+ // Alignments?
}
- if(title==null)
+ if (title == null)
{
- title = "Retrieved from " + database.getSelectedItem();
+ title = getDefaultRetrievalTitle();
}
+ SequenceFeature[] sfs = null;
+ for (Enumeration sq = al.getSequences().elements(); sq
+ .hasMoreElements();)
+ {
+ if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
+ .getSequenceFeatures()) != null)
+ {
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
- Desktop.addInternalFrame(af,
- title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ }
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
af.statusBar.setText("Successfully pasted alignment file");
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ false));
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
else
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
+ // also
+ // creates
+ // dataset
+ // sequence
+ // entries
}
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
- getHeight());
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
+ .getHeight());
alignFrame.viewport.alignment.getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.
- getAlignment().getSequences());
+ alignFrame.viewport.getAlignment().getSequences());
}
}
return al;
{
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
}
});
}
}
-
git://source.jalview.org / jalview.git / blobdiff